Single cell RNAseq analysis human TILs

Initialisation and reading data

Demultiplex samples according to HTO antibodies

Preprocessing

Filter cells with less than 200 genes and genes that are present in less than 3 cells

Remove cells that have too many mitochondrial genes expressed or too many total counts. First, plot the counts versus the percentage of mitochondrial genes and versus the number of genes to define a threshold for later filtering.

Cell cycle scoring

Principal component analysis and neighborhood graph

Clustering the neighborhood graph

Integration of CiteSeq-Data

TCR analysis scirpy

Manually annotate clonotypes with secondary chains